Rich wrote:
On 7-5-2006 13:21, Bob Hanson wrote:
Interesting. I like the way it can all be done with integers. OK, now
I have it set that it IS identifying all true molecules, and in
principle it COULD be saving some information about which atoms were
produced by which symmetry operation. Problem is, doesn't it matter
which order you apply these (redundant) symmetry operations? How does
that work? What's the convention? Or would it be enough to be able to
select "symmetry-derived sets" without the assumption of order? -
that is, I guess it would just use the order presented in the file.
BUT then I need to know in exactly what order to apply LATT to SYMM.
Right? Because I basically have two loops: "loop through the symmetry
operations" and "for each symmetry operation, loop through the LATT
translations/inversions." So is there some precise order that is
dictated by convention here?
In a CIF all of the symmetry operations are explicitly represented,
so, the number of each operation runs from 1 (identity, i.e., x,y,z)
though n for the space group (including all lattice transformations).
It is only in SHELX or, possibly PDB, where only the irreducible set
of symmetry operations are presented and the lattice transformations
are deduced. So you could take the SHELX format and simply create the
equivalent of a CIF-style list:
-- set the x,y,z operation to #1
-- add the operations from the SHELX file
-- take each of the above and add the lattice transformations to form
additional operators
This should now give identical lists of symmetry operators (including
order) for the CIF-based files and the SHELX-based files.
I don't think I'm ready to add 230 lists of symmetry operations just so
we can do this with SHELX files. Is that unreasonable? One possibility
is that we could have such a list and read it on the fly -- user
provided. Or -- oh, here's a clever idea -- have a server deliver it
from one of these sites that does this on the web. Maybe that's too
weird....
Certainly all these are produced, and the user has access to the
symmetry information, which lists the operations. Could it be that
having this list in front of you would be all you need?
Still, I wonder if there might be a "standard" order that could be
reproduced. This could be checked out at
http://www.phenix-online.org/cctbx/explore_symmetry.html by adding the
LATT and SYMM cards from .res files and comparing with XTALX.
Doe this program produce the "standard" order?
Bob
Now you only have one loop: for all symmetry operators loop over all
atoms (or vice versa depending on your preferred programing
style/efficiency).
Also, does 3555 refer to a molecule in the chemical sense, or a set
of "primitive atoms"?
It depends on if you have invoked the "connect all atoms into smallest
group on file load" option or not. Let's assume the atoms come in as a
connected molecule for now and say "primitive atoms".
The atoms are automatically connected based on Jmol bonding algorithms.
But you can change that and customize it with the "connect" command to
your heart's content. Want Al-Al bonds? sure. Want no Al-Al bonds? no
problem.
OK, but here we are talking about, for example, in quartz, TWO atoms --
one Si and one O. Right?
Naive questions:
3555
means atoms within the (0,0,0)-(1,1,1) unit cell. I get that. We're
keeping a copy of the inversion of the transformation matrix, so it's
absolutely no problem assigning abc to any atom.
What cell is {0.0, 0.0, 0.0} in?
Would you go by atom positions or the geometric center of a bonded
molecular set? That is, would you let this break up a covalently
connected molecule?
Rich
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